Contacts of the strand formed by residues 216 - 220 (chain D) in PDB entry 1I0E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 216 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D TYR* 2.8 21.9 + - - -
174D TYR 3.5 12.3 - - - -
176D LEU* 3.9 6.3 - - - -
194D PHE* 3.6 3.1 - - - -
215D ARG* 1.3 76.4 - - - +
217D ILE* 1.3 66.5 + - - -
228D TRP* 3.6 2.8 - - - -
229D VAL* 3.0 32.4 + - - +
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Residues in contact with ILE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D TYR* 3.5 1.4 - - - -
174D TYR* 2.7 45.7 + - + +
176D LEU* 4.5 7.0 - - + -
179D MET* 4.9 4.3 - - + -
187D LEU* 5.3 5.6 - - + -
192D PHE* 3.9 8.7 - - + +
193D LEU* 3.0 28.3 - - + +
194D PHE* 3.1 53.2 - - + +
216D GLY* 1.3 75.5 - - - -
218D TRP* 1.3 67.1 + - - +
219D HIS* 5.2 3.1 - - + +
226D LEU* 4.7 9.6 - - + -
227D VAL 3.6 2.7 - - - +
228D TRP* 3.2 19.7 - - + +
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Residues in contact with TRP 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D VAL* 5.2 0.7 - - - -
162D LEU* 3.1 65.6 - - + +
163D ASN* 4.1 8.5 - - - +
165D LEU* 4.0 15.3 - - + -
169D PHE 3.5 27.1 - - - -
171D GLY 3.9 10.9 - - - -
172D LYS 3.3 28.0 - - - +
173D TYR* 3.9 16.6 - - + -
217D ILE* 1.3 74.3 - - - +
219D HIS* 1.3 74.1 + - - +
220D ASN* 3.7 8.7 - - + -
225D PHE* 3.4 38.4 - + - -
226D LEU* 3.3 1.0 - - - +
227D VAL* 2.8 43.8 + - + +
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Residues in contact with HIS 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D GLY* 3.5 4.7 - - - -
172D LYS* 3.0 23.9 + - - +
174D TYR* 3.4 39.6 - + - -
187D LEU* 4.1 21.1 - - + +
192D PHE* 4.4 10.0 - + - -
217D ILE* 5.2 3.4 - - + +
218D TRP* 1.3 92.6 + - - +
220D ASN* 1.3 84.4 + - - +
221D ASP* 4.6 1.3 - - - +
223D LYS* 3.5 37.0 - - + +
225D PHE 3.4 10.5 - - - +
226D LEU* 4.0 13.0 - - + -
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Residues in contact with ASN 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D GLU 3.7 24.2 + - - +
169D PHE* 4.5 5.1 - - - -
170D LYS 3.3 15.9 - - - +
171D GLY* 3.4 2.9 - - - -
218D TRP* 3.7 5.6 - - + -
219D HIS* 1.3 94.4 + - - +
221D ASP* 1.3 60.7 + - - +
222D ASN* 3.8 5.4 - - - +
223D LYS* 2.5 32.3 + - - -
224D SER* 2.8 30.2 + - - -
225D PHE* 3.1 30.4 + - - +
252D ARG* 4.9 2.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il